đŸ”Ŧ Chimeric Detective Report

Comprehensive Analysis of Chimeric Contigs in Viral Metagenomic Assembly

28
Contigs Analyzed
8
Contigs Split
4
Contigs Preserved
0.67
Mean Confidence

📊 Summary Visualizations

Chimera Type Distribution

Confidence Score Distributions

Decision Summary

Evidence Types Overview

🔍 Detailed Analysis Results

Contig ID Chimera Type Confidence Decision Breakpoint Evidence Types Explanation
contig_003 technical_artifact 0.8 SPLIT 908 kmer_composition_change, gc_content_shift
Contig contig_003 shows clear evidence of being a technical chimera resulting from misassembly. At position 908, there is a 1.3x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.23) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.78.
contig_013 technical_artifact 0.5 PRESERVE 2922 kmer_composition_change, gc_content_shift
Contig contig_013 shows clear evidence of being a technical chimera resulting from misassembly. At position 2,922, there is a 1.0x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.27) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.76.
contig_016 technical_artifact 0.7 SPLIT 2240 kmer_composition_change, gc_content_shift
Contig contig_016 shows clear evidence of being a technical chimera resulting from misassembly. At position 2,240, there is a 1.0x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.21) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.77.
contig_018 technical_artifact 0.5 PRESERVE 6627 kmer_composition_change, gc_content_shift
Contig contig_018 shows clear evidence of being a technical chimera resulting from misassembly. At position 6,627, there is a 1.0x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.26) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.77.
chimeric_001 technical_artifact 0.7 SPLIT 1356 kmer_composition_change, gc_content_shift
Contig chimeric_001 shows clear evidence of being a technical chimera resulting from misassembly. At position 1,356, there is a 1.0x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.30) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.78.
chimeric_004 technical_artifact 0.7 SPLIT 1488 kmer_composition_change, gc_content_shift
Contig chimeric_004 shows clear evidence of being a technical chimera resulting from misassembly. At position 1,488, there is a 1.0x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.32) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.78.
cov_chimeric_003 technical_artifact 0.5 PRESERVE 926 kmer_composition_change, gc_content_shift
Contig cov_chimeric_003 shows clear evidence of being a technical chimera resulting from misassembly. At position 926, there is a 1.1x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.26) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.76.
contig_009 technical_artifact 0.7 SPLIT 3856 kmer_composition_change, gc_content_shift
Contig contig_009 shows clear evidence of being a technical chimera resulting from misassembly. At position 3,856, there is a 1.0x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.26) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.77.
contig_003 technical_artifact 0.7 SPLIT 560 kmer_composition_change, gc_content_shift
Contig contig_003 shows clear evidence of being a technical chimera resulting from misassembly. At position 560, there is a 1.1x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.21) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.79.
contig_005 technical_artifact 0.8 SPLIT 6302 kmer_composition_change, gc_content_shift
Contig contig_005 shows clear evidence of being a technical chimera resulting from misassembly. At position 6,302, there is a 1.2x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.27) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.76.
contig_008 technical_artifact 0.5 PRESERVE 5082 kmer_composition_change, gc_content_shift
Contig contig_008 shows clear evidence of being a technical chimera resulting from misassembly. At position 5,082, there is a 1.1x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.29) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.76.
contig_013 technical_artifact 1.0 PRESERVE 380 kmer_composition_change, gc_content_shift
Contig contig_013 shows clear evidence of being a technical chimera resulting from misassembly. At position 380, there is a 1.1x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.23) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.77.
contig_005 technical_artifact 0.5 SPLIT 4175 kmer_composition_change, gc_content_shift
Contig contig_005 shows clear evidence of being a technical chimera resulting from misassembly. At position 4,175, there is a 1.0x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.16) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.77.
contig_008 technical_artifact 0.5 PRESERVE 3562 kmer_composition_change, gc_content_shift
Contig contig_008 shows clear evidence of being a technical chimera resulting from misassembly. At position 3,562, there is a 1.0x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.29) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.77.
contig_018 technical_artifact 0.5 PRESERVE 6149 kmer_composition_change, gc_content_shift
Contig contig_018 shows clear evidence of being a technical chimera resulting from misassembly. At position 6,149, there is a 1.1x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.29) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.78.
contig_005 technical_artifact 0.5 SPLIT 3474 kmer_composition_change, gc_content_shift
Contig contig_005 shows clear evidence of being a technical chimera resulting from misassembly. At position 3,474, there is a 1.0x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.20) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.78.
contig_008 technical_artifact 0.5 PRESERVE 4465 kmer_composition_change, gc_content_shift
Contig contig_008 shows clear evidence of being a technical chimera resulting from misassembly. At position 4,465, there is a 1.1x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.11) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.76.
contig_012 technical_artifact 0.7 SPLIT 2003 kmer_composition_change, gc_content_shift
Contig contig_012 shows clear evidence of being a technical chimera resulting from misassembly. At position 2,003, there is a 1.0x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.29) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.77.
contig_013 technical_artifact 1.0 PRESERVE 801 kmer_composition_change, gc_content_shift
Contig contig_013 shows clear evidence of being a technical chimera resulting from misassembly. At position 801, there is a 1.6x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.18) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.78.
contig_009 technical_artifact 1.0 SPLIT 3492 kmer_composition_change, gc_content_shift
Contig contig_009 shows clear evidence of being a technical chimera resulting from misassembly. At position 3,492, there is a 1.2x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.36) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.77.
contig_003 technical_artifact 0.5 SPLIT 1028 kmer_composition_change, gc_content_shift
Contig contig_003 shows clear evidence of being a technical chimera resulting from misassembly. At position 1,028, there is a 1.0x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.22) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.76.
contig_006 technical_artifact 0.8 SPLIT 2229 kmer_composition_change, gc_content_shift
Contig contig_006 shows clear evidence of being a technical chimera resulting from misassembly. At position 2,229, there is a 1.1x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.21) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.77.
contig_009 technical_artifact 0.8 SPLIT 6261 kmer_composition_change, gc_content_shift
Contig contig_009 shows clear evidence of being a technical chimera resulting from misassembly. At position 6,261, there is a 1.3x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.26) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.75.

📈 Individual Contig Details

Click on the links below to view detailed analysis for each chimeric contig:

â„šī¸ Methodology & Interpretation

Detection Methods

Chimeric contigs are detected using multiple complementary approaches:

  • Coverage Discontinuities: Sharp changes in read coverage depth
  • Sequence Composition: Changes in GC content and k-mer frequencies
  • Taxonomic Classification: Transitions between different viral/host lineages
  • Read Pair Orientation: Inconsistent paired-end read orientations

Classification Categories

  • Technical Artifacts: Assembly errors, typically split
  • PCR Chimeras: Amplification artifacts, typically split
  • Biological Recombination: Genuine recombination events, preserved
  • Provirus Integration: Virus-host integration sites, flagged

Confidence Scores

Confidence scores range from 0-1, with higher scores indicating stronger evidence for the classification. Scores above 0.8 are considered high confidence, 0.5-0.8 medium confidence, and below 0.5 low confidence.